bugfix: struct pfold_match_type_awars changed
4 lines of code changed in 1 file:
added doxygen comments; added help; bugfix: order of amino_acids
1200 lines of code changed in 17 files:
- removed ORS here as well :)
0 lines of code changed in 1 file:
- added HELP_WRITTEN
1 lines of code changed in 1 file:
- make 'release' checks early, whether make 'save' will fail
8 lines of code changed in 1 file:
- pick helpfiles from GDEHELP/HELP_WRITTEN
12 lines of code changed in 1 file:
- help for RAxML
162 lines of code changed in 1 file:
- info about helpfiles here
7 lines of code changed in 1 file:
- note about ../HELP_WRITTEN
4 lines of code changed in 1 file:
- if helpfiles specified in GDE-MENUS exists in ./HELP_WRITTEN
do not warn about missing helpfile
(these helpfiles are processed later from ./HELP_SOURCE/genhelp/Makefile)
10 lines of code changed in 1 file:
- new parameter -commentFromFile (reads a file into tree-comment)
- fixed CL-parsing
- adds source-file and timestamp to tree-comment
65 lines of code changed in 1 file:
- don't try to export trees named '' (silently export empty tree instead)
5 lines of code changed in 1 file:
- new parameter import/consense (what to do with trees?)
- new parameter CONSTRAINT tree
- new parameter SEED (random seed for bootstrapping)
- new parameter NUMCATEGORIES (DNA only)
- if parameter TREE='' -> don't use tree
- 'rapid bootstrap analysis' and 'add new sequences (MP)' only generate
one tree. Warn and fallback to "use 1 tree".
- If INITIALREARRANGEMENT is empty -> let RAxML autodetect it
- dont specify NUMBEROFRUNS if == 1 (does not work with all RAxML algorithms)
86 lines of code changed in 1 file:
- if no result-file is found, pick bipartitions-file or
parsimonyTree-file instead
- can create consense-tree alternatively to importing
multiple trees
- writes content of RAxML-info file into ARB tree comment
100 lines of code changed in 1 file:
- delete '.'s from automatically generated tree name
2 lines of code changed in 1 file:
- moved into raxml.menu
0 lines of code changed in 2 files:
- RAxML integration (DNA and PROTEIN)
- added 'Use empirical base frequencies?' for PROTEIN
160 lines of code changed in 1 file:
- replace two flavours of raxml-menus (DNA/PROTEIN), by
one menu file handling both. The file is included twice
with different #defines
6 lines of code changed in 1 file:
- awt_get_filter() crashed when a illegal alignment was selected
(happened e.g. with alis saved in props)
Now returns a dummy filter, ARB then warns that filter is shorter than ali
30 lines of code changed in 1 file:
added some assertions
added some long casts to get SSUParc working
(yes, you can now build a pt-server and match probes with the SSUParc data base... Yippieh ;-)
10 lines of code changed in 1 file:
"int -> long"
added an assertion
2 lines of code changed in 1 file:
"0 -> NULL"
5 lines of code changed in 1 file:
- currently not used
24 lines of code changed in 1 file:
- changed linker arguments (only ARBDB is needed)
- arb_perf_test only build in DEBUG version
- compile via objects (in order to use unified compile and linker commands)
- depends updated
144 lines of code changed in 1 file:
- cleaned
0 lines of code changed in 1 file:
- use linker commands from top-makefile
- renamed object variables
44 lines of code changed in 1 file:
- changed linker commands
- fixed forwarded variables
21 lines of code changed in 1 file:
- changed linker command
- updated depends
3 lines of code changed in 1 file:
- removed call to GDE editor
0 lines of code changed in 1 file:
- don't mention gde, mapview
1 lines of code changed in 1 file:
- be more quiet
4 lines of code changed in 1 file:
- changed linker command
- depends updated
8 lines of code changed in 2 files:
- changed linker + compiler commands
- depends updated
10 lines of code changed in 4 files:
- chaged forwarded variables for new makefile
60 lines of code changed in 5 files:
- changed linker command
- removed test executable
1 lines of code changed in 1 file:
- removed CORE (last part using xview)
10 lines of code changed in 1 file:
- changed names of linker commands
54 lines of code changed in 52 files:
- removed SUN
14 lines of code changed in 1 file:
- updated overview of used DEFINES
- rewrote part defining flags, compilers, defines
- changed LINK_commands
- removed ORS
- added several dependencies
- removed OPENWIN things (no more xview)
237 lines of code changed in 1 file:
- removed some unused Fortran code from Niels
0 lines of code changed in 13 files:
- removed ORS
0 lines of code changed in 37 files:
- removed GDE GUI applications (editor, looptool, ..).
Only ARB-integrated interface remains.
Now ARB should be XView-independant
0 lines of code changed in 44 files:
- exclude GDE_proto.h
1 lines of code changed in 1 file:
- removed debug printout
0 lines of code changed in 1 file:
- comment
1 lines of code changed in 1 file:
- corrected left offset in list view (mark boxes were outside screen)
3 lines of code changed in 1 file:
- corrected set_horizontal/vertical_scrollbar_position
- disabled zoom for IRS- and List-View
- zoom-out calculation now works with dendogram as well
- Y-scrolling now works correctly with dendogram
- zoom-box:
. endposition now inside screen for dendogram (not 1 pixel outside)
. box draws correct in all 4 quadrants far radial tree
48 lines of code changed in 1 file:
- removed casted versions of GB_MEMCPY etc.
0 lines of code changed in 1 file:
- we don't support non-gnu-compilers any longer
0 lines of code changed in 1 file:
- missing \n
- removed unused code
1 lines of code changed in 1 file:
"int -> long"
"unsigned -> signed" (to find bugs easier and get -ftrapv working)
added some assertions
19 lines of code changed in 2 files:
"0 -> NULL"
added an assert
11 lines of code changed in 3 files:
- init toggler if necessary
10 lines of code changed in 1 file:
- removed useless return value
7 lines of code changed in 3 files:
- fixed path to perl skripts
5 lines of code changed in 5 files:
updated functions for protein structure comparison; added menu entry in EDIT4 for protein match settings; added help
863 lines of code changed in 14 files:
- trees were sorted the wrong way
2 lines of code changed in 1 file:
- added raxmlHPC
1 lines of code changed in 1 file:
- changed layout
27 lines of code changed in 1 file:
- AW_window::align_string() can handle labels containing '\n'
27 lines of code changed in 1 file:
- call arb_raxml-skript instead of calling raxmlHPC directly
- removed 'What to do with tree'; tree always read into ARB
by arb_raxml-skript
61 lines of code changed in 2 files:
- skript to import (some) raxml-trees
130 lines of code changed in 1 file:
- skript for calling raxmlHPC
176 lines of code changed in 1 file:
- use enum values instead of hardcoded ones
- implemented COMPRESS_NONINFO_COLUMNS
64 lines of code changed in 1 file:
- use enum values instead of hardcoded ones
13 lines of code changed in 2 files:
"long -> size_t", "int -> size_t"
3 lines of code changed in 1 file:
- moved in REPOSITORY to ../ARBTOOLS/IFTHELP
0 lines of code changed in 4 files:
"int -> long"
1 lines of code changed in 1 file:
- fixed shadow warnings
83 lines of code changed in 5 files:
- renamed MODULE defines (_ARB -> IN_ARB)
25 lines of code changed in 8 files:
Fixed/resized xpm images that cause arb_ntree and arb_edit4 to crash under Ubuntu x86_64.
800 lines of code changed in 11 files:
- assume gcc >= 3.xx
10 lines of code changed in 1 file:
- removed gcc 2.95 compat-code
1 lines of code changed in 1 file:
- dropped support for gcc 2.xx
6 lines of code changed in 1 file:
- fixed shadow warnings
42 lines of code changed in 3 files:
- indented + cleaned up
149 lines of code changed in 1 file:
- perform scrollbar calculation with integers (was done using unnecessary floats)
57 lines of code changed in 3 files:
- fixed unused-warnings
21 lines of code changed in 3 files:
- fixed shadow warnings
203 lines of code changed in 17 files:
- removed __restrict__
2 lines of code changed in 2 files:
added "__restrict__" for vectorizing loops
(don't worry, there is no aliasing)
4 lines of code changed in 2 files:
- fixed warning suppression for GDE subdirs
30 lines of code changed in 1 file:
- added -W to ARCPPLIB and ARLIB
- wrap GDEHELP output through log
6 lines of code changed in 1 file:
- indented
1692 lines of code changed in 3 files:
- updated
3 lines of code changed in 1 file:
- removed unused params
3 lines of code changed in 1 file:
- fixed shadow warning
- removed 2 unused params
13 lines of code changed in 1 file:
removing some format warnings on 32-bit
12 lines of code changed in 5 files:
"%i -> %zu"
1 lines of code changed in 1 file:
removing some format warnings
30 lines of code changed in 12 files:
- depends updated
9 lines of code changed in 1 file:
- fixed char-array-subscript
4 lines of code changed in 1 file:
- fixed shadow warnings
16 lines of code changed in 2 files:
- gb_merge -> GLOBAL_gb_merge, gb_dest -> GLOBAL_gb_dest
296 lines of code changed in 14 files:
- removed marker line from 'clean'
0 lines of code changed in 4 files:
- first build help-files in GDEHELP, then 'help'
2 lines of code changed in 1 file:
- log wasn't removed in case of error
8 lines of code changed in 4 files:
- GLOBAL_gb_main
5 lines of code changed in 1 file:
- fixed renamed global (ifdef TEST)
5 lines of code changed in 1 file:
- made local functions static
5 lines of code changed in 1 file:
- removed unused functions
0 lines of code changed in 1 file:
- removed obscure defines
- made globals static
- removed unused functions
- made local function static
3 lines of code changed in 1 file:
- removed obscure defines
- made globals static
- made local functions static
- fixed shadow warnings
- reordered functions
102 lines of code changed in 1 file:
- dos2unix, untabified, indented
926 lines of code changed in 10 files:
- shadow warning
8 lines of code changed in 1 file: